Coverage for hiperta_stream/scripts/create_base_config_structure.py: 0%
99 statements
« prev ^ index » next coverage.py v7.4.3, created at 2024-07-16 10:16 +0000
1#!/usr/bin/env python
2# P. Aubert & E. Garcia - Nov 2020, lock down Chap. II
4import tables
5import argparse
6import numpy as np
7from pkg_resources import resource_filename
10class TelescopeInformation(tables.IsDescription):
11 """
12 Class to create telescope information within r0/monitoring/telescope/information
13 """
14 nb_pixel = tables.UInt64Col()
15 nb_gain = tables.UInt64Col()
16 nb_slice = tables.UInt64Col()
17 tel_index = tables.UInt64Col()
18 tel_id = tables.UInt64Col()
19 tel_type = tables.UInt64Col()
22class CameraGeometry(tables.IsDescription):
23 """
24 Camera geometry
25 """
26 pix_id = tables.UInt64Col()
27 pix_x = tables.Float32Col()
28 pix_y = tables.Float32Col()
29 pix_area = tables.Float32Col()
32def update_calibration_data(hfile_out, gain_and_pedestal, sample_offset):
33 """
34 Reads and copies to the output file the gain, the pedestal and the unused pixels.
36 It **MUST** be the same calibration file as the file to be processed by the stream.
38 f.eg:
39 - /fefs/aswg/data/real/calibration/20201008/v05/calibration.Run2833.0000.hdf5
40 - LST-1.1.Run2833.0000.fits.fz
42 param hfile_out : obj
43 hdf5 output file to be created
44 gain_and_pedestal : str
45 Path to the calibration file to be read and copied
46 sample_offset : float
47 Offset of the pedestal we have to use for some nonsense reason
48 """
49 hfile_gain_ped = tables.open_file(gain_and_pedestal, 'r')
51 # We take the np.arrays to copy (Table with a single column not named !)
52 dc_pe = np.asarray(hfile_gain_ped.root.tel_1.calibration.col('dc_to_pe'), dtype=np.float32)[0]
53 ped = np.asarray(hfile_gain_ped.root.tel_1.calibration.col('pedestal_per_sample'), dtype=np.float32)[0]
54 unusable_pix = np.asarray(hfile_gain_ped.root.tel_1.calibration.col('unusable_pixels'), dtype=np.float32)[0]
56 ped += sample_offset
58 # Create groups in output file
59 dc_pe_group = hfile_out.create_group('/r0/monitoring/telescope', 'gain', createparents=True)
60 nonused_pix_group = hfile_out.create_group('/r0/monitoring/telescope', 'unusable_pixels', createparents=True)
62 # Copy the np.arrays (array pyTable) into the output
63 hfile_out.create_array(dc_pe_group, 'tel_001', dc_pe, 'Gain of the camera.')
64 hfile_out.create_array(nonused_pix_group, 'tel_001', unusable_pix, 'Unused pixels.')
66 # Create telescope information table (we need to create a class before). Way 1.
67 info_group = hfile_out.create_group('/r0/monitoring/telescope', 'information', createparents=True)
68 table_info_group = hfile_out.create_table(info_group, 'tel_001', TelescopeInformation, 'Telescope Information')
70 # And then add row by row all the value. Do not forget the .append() !!
71 row = table_info_group.row
72 row['nb_pixel'] = ped.shape[1]
73 row['nb_gain'] = ped.shape[0]
74 row['nb_slice'] = 40 # TODO read configuration file whenever there would be more telescopes
75 row['tel_index'] = 0 # TODO read configuration file whenever there would be more telescopes
76 row['tel_id'] = 1 # TODO read configuration file whenever there would be more telescopes
77 row['tel_type'] = 0 # TODO read configuration file whenever there would be more telescopes
78 row.append()
80 # Create ped table. Way 2.
81 ped_group = hfile_out.create_group('/r0/monitoring/telescope', 'pedestal', createparents=True) # same place as bef
82 columns_dict_pedestal = {
83 "first_event_id": tables.UInt64Col(),
84 "last_event_id": tables.UInt64Col(),
85 "pedestal": tables.Float32Col(shape=ped.shape)
86 }
88 # magic to create a description from a dictionary
89 description_pedestal = type('description columns_dict_pedestal', (tables.IsDescription,), columns_dict_pedestal)
91 table_pedestal = hfile_out.create_table(ped_group, 'tel_001', description_pedestal,
92 "Table of the pedestal for high and low gain", expectedrows=1, chunkshape=1)
94 # and lastly, add the row as always
95 tab_ped_for_entry = table_pedestal.row
96 tab_ped_for_entry["first_event_id"] = np.uint64(0)
97 tab_ped_for_entry["last_event_id"] = np.uint64(1)
98 tab_ped_for_entry["pedestal"] = ped
99 tab_ped_for_entry.append()
101 hfile_gain_ped.close()
104def update_pixel_order(hfile_out, pix_order):
105 """
106 Copies to the final h5 output file the order of pixels of the camera (injection tables; position [x] in array
107 corresponds to pixel Y in the camera).
109 Once the modules is installed, this file will ALWAYS be at
110 $PATH/hiperta_stream/config/LST-1.1.Run00442.0000_pixel_order_bin.npy
112 hfile_out : obj
113 hdf5 output file to be created
114 pix_order : str
115 Path to file that contains the injection table
117 """
118 table_pix_order = np.fromfile(pix_order, dtype=np.uint16)
120 # update table, we kill it, then we ask
121 pix_order_group = hfile_out.root.configuration.instrument.telescope.camera.pixel_order
122 pix_order_table = pix_order_group.tel_001
123 hfile_out.remove_node(pix_order_table)
125 # And add the new table at same place
126 hfile_out.create_array(pix_order_group, 'tel_001', table_pix_order, 'Pixel order of the Camera.')
129def update_camera_geometry(hfile_out):
130 """
131 Update the camera geometry with the correct one taken from ctapipe_io_lst
133 :param hfile_out: obj
134 hdf5 output file to be created
135 """
136 try:
137 from ctapipe_io_lst import load_camera_geometry
138 geometry = load_camera_geometry()
140 tabX = geometry.pix_x.value
141 tabY = geometry.pix_y.value
142 tabId = geometry.pix_id.value
143 tabArea = geometry.pix_area.value
144 nbPixel = geometry.n_pixels
145 except:
146 from hiperta_stream.dataset import get
148 tabX = np.fromfile(get('lst_proto_cam_pix_x.bin'), dtype=np.float32)
149 tabY = np.fromfile(get('lst_proto_cam_pix_y.bin'), dtype=np.float32)
150 tabId = np.fromfile(get('lst_proto_cam_pix_id.bin'), dtype=np.uint16)
151 tabArea = np.fromfile(get('lst_proto_cam_pix_area.bin'), dtype=np.float32)
152 nbPixel = tabArea.size
154 lstcam_table = hfile_out.root.configuration.instrument.telescope.camera.geometry_LSTCam
156 hfile_out.remove_node(lstcam_table)
157 # Remember to pass the parent group !!
158 new_lstcam_table = hfile_out.create_table(
159 hfile_out.root.configuration.instrument.telescope.camera, "geometry_LSTCam", CameraGeometry,
160 "LST camera geometry", expectedrows=nbPixel
161 )
163 new_lstcam_row = new_lstcam_table.row
164 for pix_area, pix_id, pix_x, pix_y in zip(tabArea, tabId, tabX, tabY):
165 new_lstcam_row['pix_area'] = pix_area
166 new_lstcam_row['pix_id'] = pix_id
167 new_lstcam_row['pix_x'] = pix_x
168 new_lstcam_row['pix_y'] = pix_y
169 new_lstcam_row.append()
172def main():
173 parser = argparse.ArgumentParser(description="Create hdf5 configuration files for hiperta_stream ")
175 parser.add_argument('--gain_pedestal', '-g', action='store', type=str,
176 dest='gain_pedestal',
177 help='Gain and pedestal hdf5 files. ',
178 required=True
179 )
181 parser.add_argument('--pixel_order', '-p', action='store', type=str,
182 dest='pixel_order',
183 help='Path to the file that contains the pixel injection table ( created with '
184 '`rta_get_zfits_pix_order`).\n'
185 'NOTE: In case of an URGENT/EMERGENCY value, an example file can be found at '
186 '$INSTALL_PATH/hiperta_stream/dataset/LST-1.1.Run00442.0000_pixel_order_bin.npy',
187 required=True
188 )
190 parser.add_argument('--config_file', '-c', action='store', type=str,
191 dest='config_file',
192 help='Path to the file that contains the `/configuration` node (gain, pedestal, pix position,'
193 'geometry ...) - stored in the config submodule of this project\n'
194 'DEFAULT: $INSTALL_PATH/hiperta_stream/dataset/default_configuration.h5',
195 default=None
196 )
198 parser.add_argument('--output_file', '-o', action='store', type=str,
199 dest='output_file',
200 help='Output filename.',
201 default='./base_structure_hdf5.h5'
202 )
204 parser.add_argument('--offset', '-s', action='store', type=float,
205 dest='sample_offset',
206 help='Offset of the pedestal.',
207 required=False,
208 default=400
209 )
211 args = parser.parse_args()
213 hout = tables.open_file(args.output_file, 'w')
214 if args.config_file is None:
215 configuration_file = resource_filename('hiperta_stream', 'dataset/default_configuration.h5')
216 else:
217 configuration_file = args.config_file
218 hin = tables.open_file(configuration_file, 'r')
220 # Copy the configuration node
221 hout.copy_node(hin.root.configuration, newparent=hout.root, recursive=True)
222 hin.close()
224 update_calibration_data(hout, args.gain_pedestal, args.sample_offset)
226 update_pixel_order(hout, args.pixel_order)
227 update_camera_geometry(hout)
229 hout.close()
232if __name__ == '__main__':
233 main()